• using R Under development (unstable) (2025-11-05 r88988)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (7)     Debian flang-new version 19.1.7 (7)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘DYNATE/DESCRIPTION’ ... OK
• this is package ‘DYNATE’ version ‘0.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [0s/1s] NOTE Maintainer: ‘Xuechan Li <xuechanli0530@gmail.com>’ The Description field contains   <arXiv:1906.07757v2> and Li, Sung and Xie (2021) <arXiv:2103.11085v2>. Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘DYNATE’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [3s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
• checking loading without being on the library search path ... [3s/4s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [20s/23s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [10s/10s] ERROR Running examples in ‘DYNATE-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Test_Leaf > ### Title: Test_Leaf The function is used to generate Leaf P-values for > ### case-control study. Users can input the leaf information through > ### argument struct_map. If there is not leaf information e.g. > ### struct_map=NULL, Test_Leaf will automatically construct leaf. > ### Argument thresh_val specifies the leaf size constructed from the > ### function. When the argument Gmat_case and Gmat_ctrl is null, > ### Test_Leaf will automatically generate those matrices. > ### Aliases: Test_Leaf > > ### ** Examples > > data("snp_dat") > > # Set leaf size M > M <- 5 > > #Construct leaves and generate leaf p-value. > p.leaf <- Test_Leaf(snp_dat=snp_dat,thresh_val=M) Error in `mutate()`: ℹ In argument: `num_unique = colsplit(num_comb, ",", c(1:2))[, 1]`. Caused by error in `levels<-`: ! factor level [112] is duplicated Backtrace:      ▆   1. ├─DYNATE::Test_Leaf(snp_dat = snp_dat, thresh_val = M)   2. │ └─DYNATE:::construct_leafs(snp_dat = snp_dat, thresh_val = thresh_val)   3. │ └─... %>% data.table()   4. ├─data.table::data.table(.)   5. ├─dplyr::mutate_at(., "Sample.Name", as.factor)   6. │ └─dplyr:::manip_at(...)   7. │ └─dplyr:::tbl_at_syms(...)   8. │ └─dplyr:::tbl_at_vars(...)   9. │ └─dplyr::tbl_vars(tbl)  10. │ ├─dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x))  11. │ │ └─base::structure(...)  12. │ └─dplyr:::tbl_vars_dispatch(x)  13. ├─dplyr::select(...)  14. ├─dplyr::mutate(., L1 = rleid(group2))  15. ├─dplyr::ungroup(.)  16. ├─dplyr::mutate(...)  17. ├─dplyr::group_by(., domainID)  18. ├─dplyr::mutate(., group = cumsum(c(-1L, diff(num_all)) <= 0L))  19. ├─dplyr::mutate(...)  20. ├─dplyr::mutate(...)  21. ├─dplyr:::mutate.data.frame(., num_unique = colsplit(num_comb, ",", c(1:2))[, 1])  22. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)  23. │ ├─base::withCallingHandlers(...)  24. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)  25. │ └─mask$eval_all_mutate(quo)  26. │ └─dplyr (local) eval()  27. ├─reshape2::colsplit(num_comb, ",", c(1:2))  28. │ ├─base::data.frame(...)  29. │ └─plyr::alply(vars, 2, type.convert, as.is = TRUE)  30. │ └─plyr:::splitter_a(.data, .margins, .expand)  31. │ └─base::lapply(dnames, function(x) factor(x, levels = x))  32. │ └─plyr (local) FUN(X[[i]], ...)  33. │ └─base::factor(x, levels = x)  34. └─base::.handleSimpleError(...)  35. └─dplyr (local) h(simpleError(msg, call))  36. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [8s/11s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘vignette.Rmd’ using rmarkdown Quitting from vignette.Rmd:46-53 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'vignette.Rmd' failed with diagnostics: ℹ In argument: `num_unique = colsplit(num_comb, ",", c(1:2))[, 1]`. Caused by error in `levels<-`: ! factor level [112] is duplicated --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed:   ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [0s/0s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs, 1 NOTE